psimi25Complex-class: Class "psimi25Complex"

In RpsiXML: R interface to PSI-MI 2.5 files

Description

A class representing complex data

Objects from the Class

Objects can be created by calls of parsePsimi25Complex

Slots

sourceDb:

Object of class "character", short label of the source database

sourceId:

Object of class "character", complex ID of the source database

shortLabel:

Object of class "character", short label of the complex

fullName:

Object of class "character", full name of the complex

interactorRef:

Object of class "character", reference ID of the interactor

organismName:

Object of class "character", orgnism name

taxId:

Object of class "character", taxonomy ID

members:

Object of class "data.frame", members (UniProt ID if available)

attributesList:

A list of attributes of the complex, each as an object of psimi25Attribute object

Methods

show

signature(object = "psimi25Complex"): shows information of the complex

sourceDb

signature(x = "psimi25Complex"): returns source database

sourceId

signature(x = "psimi25Complex"): returns source ID

attributesList

signature(x = "psimi25Complex"): returns attributes of the complex

members

signature(x = "psimi25Complex"): returns members of the complex

complexName

signature(x = "psimi25Complex"): returns complex name

Author(s)

Jitao David Zhang <[e-mail]>, Tony Chiang <[e-mail]>

See Also

parsePsimi25Complex

Examples

showClass("psimi25Complex")

Example output

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

Loading required package: RBGL
Loading required package: hypergraph

Attaching package: 'hypergraph'

The following objects are masked from 'package:AnnotationDbi':

    head, tail

The following objects are masked from 'package:S4Vectors':

    head, tail

The following objects are masked from 'package:utils':

    head, tail

No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML'
No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML'

Attaching package: 'RpsiXML'

The following object is masked from 'package:IRanges':

    members

Class "psimi25Complex" [package "RpsiXML"]

Slots:
                                                                  
Name:      shortLabel       fullName        members  interactorRef
Class:      character      character     data.frame      character
                                                                  
Name:        sourceDb       sourceId          taxId   organismName
Class:      character      character      character      character
                     
Name:  attributesList
Class:           list

Extends: "sourceDbAndId", "organismTaxIdAndName", "attributesListBase"

RpsiXML documentation built on Nov. 8, 2020, 6:02 p.m.